Advertisement

The Family Geodermatophilaceae

  • Philippe Normand
  • Daniele Daffonchio
  • Maher Gtari
Reference work entry

Abstract

Members of the family Geodermatophilaceae, order Actinomycetales, contain bacteria isolated mainly from soils, seawater, and stone surfaces that have been grouped into the three genera Geodermatophilus, Blastococcus, and Modestobacter. Members of Geodermatophilus have been found mainly in soils, Blastococcus spp. have been found in a marine sediment and in stone interiors and Modestobacter spp. have been found on stone surfaces and in polar regolith. Members of the genera Geodermatophilus and Modestobacter have been found to be unusually resistant to oxidative stresses while those of Blastococcus were found resistant to some heavy metals and metalloids. This family is close to the genera Acidothermus, Cryptosporangium, Frankia, Nakamurella, Sporichthya, and Fodinicola and was grouped with them into suborder Frankineae. A recent rearrangement has resulted in the elevation of suborder Frankineae to order Frankiales (Normand and Benson, Order VI. Frankiales ord. nov. In: Bergey’s Manual of Systematic Bacteriology, vol 5. The Actinobacteria. Bergey’s Manual Trust, Athens, pp 509–511, 2012) containing families Acidothermaceae, Cryptosporangiaceae, Frankiaceae, Geodermatophilaceae, Nakamurellaceae, Sporichthyaceae, and Fodinicola.

Keywords

Type Strain Aerial Mycelium Biological Soil Crust Stone Surface Stone Material 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Ahrens R, Moll G (1970) Ein neues knospendes Bakterium aus der Ostsee. (A new budding bacterium from the Baltic Sea). Arch Mikrobiol 70:243–265PubMedCrossRefGoogle Scholar
  2. Akkermans A, Hahn D, Baker D (1992) The family Frankiaceae. In: Balows A, Truper H, Dworkin M, Harder W, Schleifer K-H (eds) The prokaryotes: a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications. Springer, New York, pp 1069–1084Google Scholar
  3. Amato P, Parazols M, Sancelme M, Laj P, Mailhot G, Delort AM (2007a) Microorganisms isolated from the water phase of tropospheric clouds at the Puy de Dome: major groups and growth abilities at low temperatures. FEMS Microbiol Ecol 59:242–254PubMedCrossRefGoogle Scholar
  4. Amato P, Hennebelle R, Magand O, Sancelme M, Delort AM, Barbante C et al (2007b) Bacterial characterization of the snow cover at Spitzberg, Svalbard. FEMS Microbiol Ecol 59:255–264PubMedCrossRefGoogle Scholar
  5. Babalola OO, Kirby BM, Le Roes-Hill M, Cook AE, Cary SC, Burton SG, Cowan DA (2009) Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils. Environ Microbiol 11:566–576PubMedCrossRefGoogle Scholar
  6. Bagwell CE, Bhat S, Hawkins GM, Smith BW, Biswas T, Hoover TR et al (2008) Survival in nuclear waste, extreme resistance, and potential applications gleaned from the genome sequence of Kineococcus radiotolerans SRS30216. PLoS One 3:e3878PubMedCentralPubMedCrossRefGoogle Scholar
  7. Bordenave S, Goni-Urriza MS, Caumette P, Duran R (2007) Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl Environ Microbiol 73:6089–6097PubMedCentralPubMedCrossRefGoogle Scholar
  8. Brusetti L, Malkhazova I, Gtari M, Tamagnini I, Borin S, Merabishvili M et al (2008) Fluorescent-BOX-PCR for resolving bacterial genetic diversity, endemism and biogeography. BMC Microbiol 8:220PubMedCentralPubMedCrossRefGoogle Scholar
  9. Bunt JS, Rovira AD (1955) Microbiological studies of some subantarctic soils. J Soil Sci 6:119–128CrossRefGoogle Scholar
  10. Callegan RP, Nobre MF, McTernan PM, Battista JR, Navarro-Gonzalez R, McKay CP et al (2008) Description of four novel psychrophilic, ionizing radiation-sensitive Deinococcus species from alpine environments. Int J Syst Evol Microbiol 58:1252–1258PubMedCrossRefGoogle Scholar
  11. Cash HL, Whitham CV, Behrendt CL, Hooper LV (2006) Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science 313:1126–1130PubMedCentralPubMedCrossRefGoogle Scholar
  12. Chanal A, Chapon V, Benzerara K, Barakat M, Christen R, Achouak W et al (2006) The desert of Tataouine: an extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. Environ Microbiol 8:514–525PubMedCrossRefGoogle Scholar
  13. Cheng SM, Foght JM (2007) Cultivation-independent and -dependent characterization of bacteria resident beneath John Evans Glacier. FEMS Microbiol Ecol 59:318–330PubMedCrossRefGoogle Scholar
  14. Chevrot R, Rosen R, Haudecoeur E, Cirou A, Shelp BJ, Ron E, Faure D (2006) GABA controls the level of quorum-sensing signal in Agrobacterium tumefaciens. Proc Natl Acad Sci U S A 103:7460–7464PubMedCentralPubMedCrossRefGoogle Scholar
  15. Chouaia B, Crotti E, Brusetti L, Daffonchio D, Essoussi I, Nouioui I et al (2012) Genome sequence of Blastococcus saxobsidens DD2, a stone inhabiting bacterium. J Bacteriol 194:2752–2753PubMedCentralPubMedCrossRefGoogle Scholar
  16. Chuvochina MS, Alekhina I, Normand P, Petit JR, Bulat S (2011a) Three events of saharan dust deposition on the Mont-Blanc glacier associated with different snow-colonizing bacterial phylotypes. Mikrobiologiya 80:129–135Google Scholar
  17. Chuvochina MS, Marie D, Chevaillier S, Petit JR, Normand P, Alekhina IA, Bulat SA (2011b) Community variability of bacteria in alpine snow (Mont Blanc) containing Saharan dust deposition and their snow colonisation potential. Microbes Environ 26:237–247PubMedCrossRefGoogle Scholar
  18. De Graef B, Cnudde V, Dick J, De Belie N, Jacobs P, Verstraete W (2005) A sensitivity study for the visualisation of bacterial weathering of concrete and stone with computerised X-ray microtomography. Sci Total Environ 341:173–183PubMedCrossRefGoogle Scholar
  19. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142PubMedCrossRefGoogle Scholar
  20. Eppard M, Krumbein WE, Koch C, Rhiel E, Staley JT, Stackebrandt E (1996) Morphological, physiological, and molecular characterization of actinomycetes isolated from dry soil, rocks, and monument surfaces. Arch Microbiol 166:12–22PubMedCrossRefGoogle Scholar
  21. Essoussi I, Ghodhbane-Gtari F, Amairi H, Sghaier H, Jaouani A, Brusetti L Gtari M (2010) Esterase as an enzymatic signature of Geodermatophilaceae adaptability to Sahara desert stones and monuments. J Appl Microbiol 108(5):1723–1732PubMedCrossRefGoogle Scholar
  22. Essoussi I, Boujmil R, Nouioui I, Abbassi-Ghozzi I, Hamza A, Boudabous A, Gtari M (2012) Genetic diversity and esterase-profiling of actinobacteria isolated from Sahara desert stones and monuments. Geomicrobiology Journal 29(1):23–28CrossRefGoogle Scholar
  23. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229CrossRefGoogle Scholar
  24. Fredrickson JK, Li SM, Gaidamakova EK, Matrosova VY, Zhai M, Sulloway HM et al (2008) Protein oxidation: key to bacterial desiccation resistance? ISME J 2:393–403PubMedCrossRefGoogle Scholar
  25. Garrity GM, Heimbuch BK, Gagliardi M (1996) Isolation of zoosporogenous actinomycetes from desert soils. J Ind Microbiol Biotechnol 17:260–267CrossRefGoogle Scholar
  26. Gomez-Alarcon G, de la Torre MA (1994) Mechanisms of microbial corrosion on petrous materials. Microbiologia 10:111–120PubMedGoogle Scholar
  27. Gorbushina AA (2007) Life on the rocks. Environ Microbiol 9:1613–1631PubMedCrossRefGoogle Scholar
  28. Gordon MA, Perrin U (1971) Pathogenicity of Dermatophilus and Geodermatophilus. Infect Immun 4:29–33PubMedCentralPubMedGoogle Scholar
  29. Gtari M, Essoussi I, Maaoui R, Sghaier H, Boujmil R, Gury J et al (2012) Contrasted resistance of stone-dwelling Geodermatophilaceae species to stresses known to give rise to reactive oxygen species. FEMS Microbiol Ecol 80:566–577PubMedCrossRefGoogle Scholar
  30. Hahn D, Lechevalier M, Fischer A, Stackebrandt E (1989) Evidence for a close phylogenetic relationship between members of the genera Frankia, Geodermatophilus, and “Blastococcus” and emendation of the family Frankiaceae. Syst Appl Microbiol 11:236–242CrossRefGoogle Scholar
  31. Hervas A, Casamayor EO (2009) High similarity between bacterioneuston and airborne bacterial community compositions in a high mountain lake area. FEMS Microbiol Ecol 67:219–228PubMedCrossRefGoogle Scholar
  32. Hervas A, Camarero L, Reche I, Casamayor EO (2009) Viability and potential for immigration of airborne bacteria from Africa that reach high mountain lakes in Europe. Environ Microbiol 11:1612–1623PubMedCrossRefGoogle Scholar
  33. Hoehenwarter W, Tang Y, Ackermann R, Pleissner KP, Schmid M, Stein R et al (2008) Identification of proteins that modify cataract of mouse eye lens. Proteomics 8:5011–5024PubMedCentralPubMedCrossRefGoogle Scholar
  34. Ishiguro EE, Wolfe RS (1970) Control of morphogenesis in Geodermatophilus: ultrastructural studies. J Bacteriol 104:566–580PubMedCentralPubMedGoogle Scholar
  35. Ivanova N, Sikorski J, Jando M, Munk C, Lapidus A, Glavina Del Rio T et al (2010) Complete genome sequence of Geodermatophilus obscurus type strain (G-20T). Stand Genomic Sci 2:158–167PubMedCentralPubMedCrossRefGoogle Scholar
  36. Jaouani A, Neifar M, Hamza A, Chaabouni S, Martinez MJ, Gtari M (2012) Purification and characterization of a highly thermostable esterase from the actinobacterium Geodermatophilus obscurus strain G20. J Basic Microbiol 52:653–660PubMedCrossRefGoogle Scholar
  37. Kumar A, Hazlett LD, Yu FS (2008) Flagellin suppresses the inflammatory response and enhances bacterial clearance in a murine model of Pseudomonas aeruginosa keratitis. Infect Immun 76:89–96PubMedCentralPubMedCrossRefGoogle Scholar
  38. Lapouge K, Schubert M, Allain FH, Haas D (2008) Gac/Rsm signal transduction pathway of gamma-proteobacteria: from RNA recognition to regulation of social behaviour. Mol Microbiol 67:241–253PubMedCrossRefGoogle Scholar
  39. Lechevalier MP (1989) Actinomycetes with multilocular sporangia. In: ST Williams MS, Holt JE (eds) Bergey’s manual of systematic bacteriology. Williams and Wilkins, Baltimore, pp 2405–2410Google Scholar
  40. Lee SD (2006) Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970. Int J Syst Evol Microbiol 56:2391–2396PubMedCrossRefGoogle Scholar
  41. Liao PC, Huang BH, Huang S (2007) Microbial community composition of the Danshui river estuary of Northern Taiwan and the practicality of the phylogenetic method in microbial barcoding. Microb Ecol 54:497–507PubMedCrossRefGoogle Scholar
  42. Login FH, Balmand S, Vallier A, Vincent-Monegat C, Vigneron A, Weiss-Gayet M et al (2011) Antimicrobial peptides keep insect endosymbionts under control. Science 334:362–365PubMedCrossRefGoogle Scholar
  43. Luedemann GM (1968) Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). J Bacteriol 96:1848–1858PubMedCentralPubMedGoogle Scholar
  44. Luedemann GM, Fonseca AF (1989) Genus Geodermatophilus Luedemann 1968. Williams and Wilkins, Baltimore, pp 2406–2409Google Scholar
  45. Mandel M, Marmur J (1968) Use of ultraviolet absorbance/temperature profile for detecting guanidine plus cytosine content of DNA. In Moldave LGK (ed) Methods in enzymology. Academic Press, London, pp 195–206Google Scholar
  46. Manickam N, Reddy MK, Saini HS, Shanker R (2008) Isolation of hexachlorocyclohexane-degrading Sphingomonas sp. by dehalogenase assay and characterization of genes involved in gamma-HCH degradation. J Appl Microbiol 104:952–960PubMedCrossRefGoogle Scholar
  47. Markert S, Arndt C, Felbeck H, Becher D, Sievert SM, Hugler M et al (2007) Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila. Science 315:247–250PubMedCrossRefGoogle Scholar
  48. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167CrossRefGoogle Scholar
  49. Mevs U, Stackebrandt E, Schumann P, Gallikowski CA, Hirsch P (2000) Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains). Int J Syst Evol Microbiol 50:337–346PubMedCrossRefGoogle Scholar
  50. Meyer B, Kuever J (2007) Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment using aprA as functional marker gene. Appl Environ Microbiol 73:7664PubMedCentralPubMedCrossRefGoogle Scholar
  51. Montero-Calasanz MC, Goker M, Potter G, Rohde M, Sproer C, Schumann P et al (2012) Geodermatophilus arenarius sp. nov., a xerophilic actinomycete isolated from Saharan desert sand in Chad. Extremophiles 16:903–909PubMedCrossRefGoogle Scholar
  52. Montero-Calasanz MC, Goker M, Rohde M, Schumann P, Potter G, Sproer C et al (2013) Geodermatophilus siccatus sp. nov., isolated from arid sand of the Saharan desert in Chad. Antonie Van Leeuwenhoek 103:449–456CrossRefGoogle Scholar
  53. Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, Hattori M (2006) The 160-kilobase genome of the bacterial endosymbiont Carsonella. Science 314:267Google Scholar
  54. Nie GX, Ming H, Li S, Zhou EM, Cheng J, Yu TT et al (2012) Geodermatophilus nigrescens sp. nov., isolated from a dry-hot valley. Antonie Van Leeuwenhoek 101:811–817PubMedCrossRefGoogle Scholar
  55. Normand P (2006) Geodermatophilaceae fam. nov., a formal description. Int J Syst Evol Microbiol 56:2277–2278PubMedCrossRefGoogle Scholar
  56. Normand P, Benson DR (2012a) Family IV. Geodermatophilaceae Normand 2006, 2277VP (Effective publication: Normand, Orso, Cournoyer, Jeannin, Chapelon, Dawson, Evtushenko and Misra 1996, 8) Springer, New York, p 699. In: Bergey’s manual of systematic bacteriology, vol 5, 2nd edn, the Actinobacteria. Goodfellow MKP, Busse H-J, Trujillo ME, Ludwig W, Suzuki KIPA (eds). Springer, New YorkGoogle Scholar
  57. Normand P, Benson DR (2012b) The Actinobacteria, vol 5. Bergey’s Manual Trust, Athens, pp 509–511Google Scholar
  58. Normand P, Orso S, Cournoyer B, Jeannin P, Chapelon C, Dawson J et al (1996) Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int J Syst Bacteriol 46:1–9PubMedCrossRefGoogle Scholar
  59. Normand P, Gury J, Pujic P, Chouaia B, Crotti E, Brusetti L et al (2012) Genome sequence of radio-resistant Modestobacter marinus strain BC501, a representative actinobacterium thriving on calcareous stone surfaces. J Bacteriol 194:4773PubMedCentralPubMedCrossRefGoogle Scholar
  60. Qin S, Bian G-K, Zhang Y-J, Xing K, Cao C-L, Liu C-H et al (2013) Modestobacter roseus sp. nov., an endophytic actinomycete isolated from the coastal halophyte Salicornia europaea Linn., and emended description of the genus Modestobacter. IJSEM 63:2197–2202PubMedGoogle Scholar
  61. Rainey FA, Ray K, Ferreira M, Gatz BZ, Nobre MF, Bagaley D et al (2005) Extensive diversity of ionizing-radiation-resistant bacteria recovered from Sonoran Desert soil and description of nine new species of the genus Deinococcus obtained from a single soil sample. Appl Environ Microbiol 71:5225–5235PubMedCentralPubMedCrossRefGoogle Scholar
  62. Reddy GS, Potrafka RM, Garcia-Pichel F (2007) Modestobacter versicolor sp. nov., an actinobacterium from biological soil crusts that produces melanins under oligotrophy, with emended descriptions of the genus Modestobacter and Modestobacter multiseptatus Mevs et al. 2000. Int J Syst Evol Microbiol 57:2014–2020PubMedCrossRefGoogle Scholar
  63. Ryjenkov DA, Tarutina M, Moskvin OV, Gomelsky M (2005) Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain. J Bacteriol 187:1792–1798PubMedCentralPubMedCrossRefGoogle Scholar
  64. Salazar O, Valverde A, Genilloud O (2006) Real-time PCR for the detection and quantification of Geodermatophilaceae from stone samples and identification of new members of the genus Blastococcus. Appl Environ Microbiol 72:346–352PubMedCentralPubMedCrossRefGoogle Scholar
  65. Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340CrossRefGoogle Scholar
  66. Stackebrandt E, Schumann P (2012) Genus II. Blastococcus Ahrens and Moll 1970, 264AL emend. Urzì, Salamone, Schumann, Rohde and Stackebrandt 2004b, 257 emend. Lee 2006, 2394. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Ludwig W, Suzuki KI, Parte A (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn, the Actinobacteria. Springer, New York, pp 529–534Google Scholar
  67. Stackebrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491CrossRefGoogle Scholar
  68. Staley JT (1968) Prosthecomicrobium and Ancalomicrobium: new prosthecate freshwater bacteria. J Bacteriol 95:1921–1942PubMedCentralPubMedGoogle Scholar
  69. Taylor-George S, Palmer F, Staley JT, Borns DJ, Curtiss B (1983) Fungi and bacteria involved in desert varnish formation. Microb Ecol 9:227–245PubMedCrossRefGoogle Scholar
  70. Torsvik V, Ovreas L, Thingstad TF (2002) Prokaryotic diversity–magnitude, dynamics, and controlling factors. Science 296:1064–1066PubMedCrossRefGoogle Scholar
  71. Urzì C, Realini M (1998) Colour changes of Noto’s calcareous sandstone as related to its colonisation by microorganisms. Int Biodeter Biodegr 42:45–54CrossRefGoogle Scholar
  72. Urzì C, Brusetti L, Salamone P, Sorlini C, Stackebrandt E, Daffonchio D (2001) Biodiversity of Geodermatophilaceae isolated from altered stones and monuments in the Mediterranean basin. Environ Microbiol 3:471–479PubMedCrossRefGoogle Scholar
  73. Urzi C, Salamone P, Schumann P, Rohde M, Stackebrandt E (2004) Blastococcus saxobsidens sp. nov., and emended descriptions of the genus Blastococcus Ahrens and Moll 1970 and Blastococcus aggregatus Ahrens and Moll 1970. Int J Syst Evol Microbiol 54:253–259PubMedCrossRefGoogle Scholar
  74. Welton RG, Cuthbert SJ, McLean R, Hursthouse A, Hughes J (2003) A preliminary study of the phycological degradation of natural stone masonry. Environ Geochem Health 25:139–145PubMedCrossRefGoogle Scholar
  75. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN et al (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056–1060PubMedCentralPubMedCrossRefGoogle Scholar
  76. Xiang S, Yao T, An L, Xu B, Wang J (2005) 16S rRNA sequences and differences in bacteria isolated from the Muztag Ata glacier at increasing depths. Appl Environ Microbiol 71:4619–4627PubMedCentralPubMedCrossRefGoogle Scholar
  77. Xiao J, Luo Y, Xu J, Xie S, Xu J (2011) Modestobacter marinus sp. nov., a psychrotolerant actinobacterium from deep-sea sediment, and emended description of the genus Modestobacter. Int J Syst Evol Microbiol 61:1710–1714PubMedCrossRefGoogle Scholar
  78. Yarza P, Ludwig W, Euzeby J, Amann R, Schleifer KH, Glockner FO, Rossello-Mora R (2010) Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291–299PubMedCrossRefGoogle Scholar
  79. Yuan M, Zhang W, Dai S, Wu J, Wang Y, Tao T et al (2009) Deinococcus gobiensis sp. nov., an extremely radiation-resistant bacterium. Int J Syst Evol Microbiol 59:1513–1517PubMedCrossRefGoogle Scholar
  80. Zhang YQ, Chen J, Liu HY, Zhang YQ, Li WJ, Yu LY (2011) Geodermatophilus ruber sp. nov., isolated from rhizosphere soil of a medicinal plant. Int J Syst Evol Microbiol 61:190–193PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Philippe Normand
    • 1
  • Daniele Daffonchio
    • 2
  • Maher Gtari
    • 3
  1. 1.Ecologie Microbienne, Centre National de la Recherche Scientifique UMR 5557Université Lyon IVilleurbanne, CedexFrance
  2. 2.Dipartimento di Scienze per gli Alimenti la Nutrizione e l’Ambiente (DeFENS)Università degli Studi di MilanoMilanItaly
  3. 3.Laboratoire Microorganismes et Biomolécules ActivesUniversité de Tunis El Manar (FST) et Université de Carthage (ISSTE)TunisTunisia

Personalised recommendations